[2024-01-24 10:57:13,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,378] [INFO] DQC Reference Directory: /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference
[2024-01-24 10:57:14,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,793] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg403ba160-9283-424c-b6b0-5e25058eec13/GCF_020829495.1_ASM2082949v1_genomic.fna.gz | prodigal -d GCF_020829495.1_ASM2082949v1_genomic.fna/cds.fna -a GCF_020829495.1_ASM2082949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:31,855] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:31,855] [INFO] Task started: HMMsearch
[2024-01-24 10:57:31,855] [INFO] Running command: hmmsearch --tblout GCF_020829495.1_ASM2082949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/reference_markers.hmm GCF_020829495.1_ASM2082949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,318] [INFO] Found 6/6 markers.
[2024-01-24 10:57:32,388] [INFO] Query marker FASTA was written to GCF_020829495.1_ASM2082949v1_genomic.fna/markers.fasta
[2024-01-24 10:57:32,389] [INFO] Task started: Blastn
[2024-01-24 10:57:32,389] [INFO] Running command: blastn -query GCF_020829495.1_ASM2082949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/reference_markers.fasta -out GCF_020829495.1_ASM2082949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,097] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,100] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:33,100] [INFO] Target genome list was writen to GCF_020829495.1_ASM2082949v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,106] [INFO] Task started: fastANI
[2024-01-24 10:57:33,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg403ba160-9283-424c-b6b0-5e25058eec13/GCF_020829495.1_ASM2082949v1_genomic.fna.gz --refList GCF_020829495.1_ASM2082949v1_genomic.fna/target_genomes.txt --output GCF_020829495.1_ASM2082949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:05,719] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:05,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:05,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:05,731] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:05,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:05,732] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	100.0	2714	2720	95	conclusive
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	88.4941	1768	2720	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	78.2229	824	2720	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	78.1567	824	2720	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.6915	619	2720	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.4906	725	2720	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.4891	712	2720	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.4545	728	2720	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.44	681	2720	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.3842	577	2720	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	77.2974	644	2720	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	76.2899	152	2720	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.9035	97	2720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:05,733] [INFO] DFAST Taxonomy check result was written to GCF_020829495.1_ASM2082949v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:05,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:05,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:05,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/checkm_data
[2024-01-24 10:58:05,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:05,815] [INFO] Task started: CheckM
[2024-01-24 10:58:05,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020829495.1_ASM2082949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020829495.1_ASM2082949v1_genomic.fna/checkm_input GCF_020829495.1_ASM2082949v1_genomic.fna/checkm_result
[2024-01-24 10:58:58,571] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:58,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:58,594] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:58,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:58,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020829495.1_ASM2082949v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:58,595] [INFO] Task started: Blastn
[2024-01-24 10:58:58,596] [INFO] Running command: blastn -query GCF_020829495.1_ASM2082949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge85747a2-49e7-4de6-a401-fe5ea420a552/dqc_reference/reference_markers_gtdb.fasta -out GCF_020829495.1_ASM2082949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:59,499] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:59,503] [INFO] Selected 25 target genomes.
[2024-01-24 10:58:59,503] [INFO] Target genome list was writen to GCF_020829495.1_ASM2082949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:59,532] [INFO] Task started: fastANI
[2024-01-24 10:58:59,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg403ba160-9283-424c-b6b0-5e25058eec13/GCF_020829495.1_ASM2082949v1_genomic.fna.gz --refList GCF_020829495.1_ASM2082949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020829495.1_ASM2082949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:11,982] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:12,008] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:00:12,008] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002813575.1	s__Nostoc flagelliforme_A	93.0559	1999	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443655.1	s__Nostoc sphaeroides	92.1972	1768	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.62	98.62	0.92	0.92	2	-
GCF_003113895.1	s__Nostoc commune	91.8018	1915	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014696655.1	s__Nostoc sp014696655	90.6004	1760	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698795.1	s__Nostoc sp014698795	90.3408	1827	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698505.1	s__Nostoc foliaceum_A	90.2019	1808	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.20	96.44	0.93	0.87	3	-
GCA_017114985.1	s__Nostoc sp017114985	89.6297	1681	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698065.1	s__Nostoc flagelliforme_B	89.0524	1818	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014023275.1	s__Nostoc edaphicum_A	88.7992	1756	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115105.1	s__Nostoc sp017115105	88.7895	1674	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.81	99.81	0.95	0.95	2	-
GCA_017114945.1	s__Nostoc sp017114945	88.7721	1636	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017114995.1	s__Nostoc sp017114995	88.7364	1720	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014222285.1	s__Nostoc sp014222285	88.7282	1679	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712795.1	s__Nostoc sp001712795	88.7026	1759	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698035.1	s__Nostoc muscorum	88.5385	1754	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.16	95.01	0.81	0.79	7	-
GCF_000020025.1	s__Nostoc punctiforme	88.4999	1766	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949795.1	s__Nostoc sp002949795	88.4589	1695	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949735.1	s__Nostoc sp002949735	88.3715	1785	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.73	95.05	0.82	0.76	3	-
GCA_017115085.1	s__Nostoc sp017115085	88.3176	1689	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115165.1	s__Nostoc sp017115165	88.3162	1774	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207245.1	s__Nostoc edaphicum_B	88.2212	926	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393905.1	s__Nostoc sp013393905	87.6379	1782	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015714725.1	s__Nostoc sp015714725	87.0067	1547	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697355.1	s__Nostoc calcicola	84.6306	1682	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.97	99.97	0.98	0.98	2	-
GCF_010091925.1	s__Nostoc sp010091925	83.0682	1506	2720	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:12,010] [INFO] GTDB search result was written to GCF_020829495.1_ASM2082949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:12,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:12,015] [INFO] DFAST_QC result json was written to GCF_020829495.1_ASM2082949v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:12,015] [INFO] DFAST_QC completed!
[2024-01-24 11:00:12,015] [INFO] Total running time: 0h2m59s